{"id":"https://openalex.org/W2138071529","doi":"https://doi.org/10.1093/bioinformatics/bts297","title":"<i>Gossamer</i> \u2014 a resource-efficient <i>de novo</i> assembler","display_name":"<i>Gossamer</i> \u2014 a resource-efficient <i>de novo</i> assembler","publication_year":2012,"publication_date":"2012-05-18","ids":{"openalex":"https://openalex.org/W2138071529","doi":"https://doi.org/10.1093/bioinformatics/bts297","mag":"2138071529","pmid":"https://pubmed.ncbi.nlm.nih.gov/22611131"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts297","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts297","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046030886","display_name":"Thomas Conway","orcid":"https://orcid.org/0000-0003-3966-5109"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Thomas Conway","raw_affiliation_strings":["NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046963746","display_name":"Jeremy Wazny","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jeremy Wazny","raw_affiliation_strings":["NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018478843","display_name":"Andrew Bromage","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew Bromage","raw_affiliation_strings":["NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041495909","display_name":"Justin Zobel","orcid":"https://orcid.org/0000-0001-6622-032X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Justin Zobel","raw_affiliation_strings":["NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020223445","display_name":"Bryan Beresford\u2010Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I42894916","display_name":"Data61","ror":"https://ror.org/03q397159","country_code":"AU","type":"other","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I42894916","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Bryan Beresford-Smith","raw_affiliation_strings":["NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NICTA Victoria Research Laboratory, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046030886"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I42894916"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9818,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.74324213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"14","first_page":"1937","last_page":"1938"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8737999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8737999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.01720000058412552,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.013700000010430813,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.7723358869552612},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7606502771377563},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5365989208221436},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.5229214429855347},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4706997871398926},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4703505337238312},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.4407351016998291},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3398738503456116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18316316604614258},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1607368290424347},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0741337239742279},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07307296991348267}],"concepts":[{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7723358869552612},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7606502771377563},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5365989208221436},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.5229214429855347},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4706997871398926},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4703505337238312},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.4407351016998291},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3398738503456116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18316316604614258},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1607368290424347},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0741337239742279},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07307296991348267},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts297","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts297","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22611131","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22611131","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W1982827785","https://openalex.org/W2023911006","https://openalex.org/W2097529842","https://openalex.org/W2115501618","https://openalex.org/W2127768708","https://openalex.org/W2133531097","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2171475724"],"related_works":["https://openalex.org/W4387083702","https://openalex.org/W3021840362","https://openalex.org/W2962743744","https://openalex.org/W3009176350","https://openalex.org/W3090794301","https://openalex.org/W3167837387","https://openalex.org/W2952788979","https://openalex.org/W2951195494","https://openalex.org/W2580258113","https://openalex.org/W4386105821"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,15],"de":[2,87],"novo":[3],"assembly":[4,91],"of":[5,17,35,85,99],"short":[6,48],"read":[7],"high-throughput":[8],"sequencing":[9,36],"data":[10,18],"poses":[11],"significant":[12,33],"computational":[13],"challenges.":[14],"volume":[16],"is":[19,111,120],"huge;":[20],"the":[21,27,86,96],"reads":[22],"are":[23,32,39,52],"tiny":[24],"compared":[25],"to":[26,46,55,90,95],"underlying":[28],"sequence,":[29],"and":[30,70,114],"there":[31],"numbers":[34],"errors.":[37],"There":[38],"numerous":[40],"software":[41],"packages":[42],"that":[43,92,109],"allow":[44],"users":[45],"assemble":[47],"reads,":[49],"but":[50,101],"most":[51],"either":[53],"limited":[54],"relatively":[56],"small":[57],"genomes":[58],"(e.g.":[59],"bacteria)":[60],"or":[61,66],"require":[62],"large":[63],"computing":[64],"infrastructure":[65],"employ":[67],"greedy":[68],"algorithms":[69],"thus":[71],"often":[72],"do":[73],"not":[74],"yield":[75],"high-quality":[76,116],"results.":[77],"RESULTS:":[78],"We":[79],"have":[80],"developed":[81],"Gossamer,":[82],"an":[83],"implementation":[84],"Bruijn":[88],"approach":[89],"requires":[93],"close":[94],"theoretical":[97],"minimum":[98],"memory,":[100],"still":[102],"allows":[103],"efficient":[104,113],"processing.":[105],"Our":[106],"results":[107],"show":[108],"it":[110],"space":[112],"produces":[115],"assemblies.":[117],"AVAILABILITY:":[118],"Gossamer":[119],"available":[121],"for":[122],"non-commercial":[123],"use":[124],"from":[125],"http://www.genomics.csse.unimelb.edu.au/product-gossamer.php.":[126]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2016-06-24T00:00:00"}
